ROOTs of the Tree
by CrimsonCrossOfShame
Summary: A more militristic Konoha and a stronger smarter Naruto. A member of a whole new ROOT program, see Naruto progress as the jinchuriki of the Kyuubi no Kitsune as a weapon of Konoha. Alternate Universe and no pairings as of yet if ever.
1. Chapter 1

**AN: I don't really expect anything to come of this, it's really just a blah I came up with reading another story thinking that the villages, while military villages aren't very militaristic and I want to give it a much darker induction. **

**The academy students will be trained much harder, Naruto himself will be considered a weapon and he will know it. **

**Story will be very AU and more than likely no pairing and if there is it might be Naruto/Temari simply because her brother is also a Jinchuriki and she might be more comfortable, that and Naruto will be much more serious. **

**Root will exist, but it will be totally different. **

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Ok, so onward with the story…

**ROOTS OF THE TREE**

Chapter One

The Dawn…

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It was roughly around four twenty hours when the child of eight woke for his morning rituals which consisted of washing his mop of yellow hair and brushing his teeth. The boys name was Naruto and he was a shinobi in training.

The child had been in training for the last two years since he was six years old and would graduate at the end of this year and be incorporated in to the ANBU ranks and deployed into the heavier combat zones if the need arose.

Naruto Uzumaki was the Jinchuriki of the Kyuubi no Kitsune the most powerful of the nine Biju, demon lords of massive destructive power that could consume the world in fire. The Kyuubi had attacked the village of Konoha and with the sacrifice of their greatest leader, the Yondaime Hokage, the beast was sealed into the naval of the newly born Naruto.

Naruto would become Konoha's ace.

Normal children were placed into the academy at the age of nine and graduated at the age twelve and placed under a Jounin instructor in a team of three until they made Chuunin. Naruto however was placed in a much more challenging physical and mental regiment with a select few others of varying ages.

These few would be promoted to Chuunin upon graduation and placed into ANBU.

Finishing with his mundane morning ritual, the eight year old dressed in a black long sleeve shirt that also doubled as a half mask concealing his whisker scared cheeks, mouth, and nose. He also wore black pants, black ninja sandals with his ankles bandaged, and black fingerless gloves that went to mid wrist.

As far as weapons go he wore a simple kunai pouch around his left leg and a tanto strapped to his back.

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Naruto arrived at the ANBU headquarters at O five hundred hours and reported to his class room. Walking to his seat he nodded to a few members of his squad before sitting down and waiting for the ANBU instructor.

There was a total of twenty people in the room, four squads of five. These twenty were this generation's ROOT a program ran by the commanders of ANBU, Danzo, and the Hokage himself.

The four squad leaders were as follows in order: first squad leader Uchiha Sasuke, second squad leader Nara Shikamaru, third squad leader Ichimaru Sai, and fourth squad leader Uzumaki Naruto.

His squad consisted of Ino Yamanaka, interrogation specialist, Rika Uchiha, combat, Disasuke Aburame, espionage, and Neji Hyuuga, reconnaissance.

A few minutes later the Shinobi in training snapped to attention as the ANBU instructor entered the room.

"Take Seat", the ANBU ordered," Now, for the next few weeks you will be taking mission as a squad to gain the necessary experience to become Chuunin. The missions will be C rank in nature and you will have a supervising ANBU escort, is this clear?"

"Sir, yes sir"

"Alright, on my command go to the court yard and meet up with your ANBU supervisor before reporting to Hokage-sama. Fall out."

Naruto with his squad in tow stood from their seats and exited the class room.

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Four ANBU stood in the court yard awaiting the shinobi to be. Who upon sight moved to intercept the squads they would be supervising.

"Squad four," called an ANBU wearing a tiger mask," Fall in."

The squad did as told with Naruto falling in on the far right followed by Ino to his left Rika to hers, Disasuke, and finally Neji all at the position of attention.

"At ease" the ANBU called falling into the relaxed stance as well," I will be supervising your missions for the next two months and training you to a more ready level as well during the time frame. I will NOT interfere in your mission unless one of your lives is at risk; furthermore this will be a test of Uzumaki's leadership and the individual skills of each and every one of you. Understood?"

"Sir, yes sir."

"Alright, by my watch it is 0 five thirty hours, you have till 0 six hundred hours to eat chow and report as a squad to Hokage Tower. Understood?"

"Sir, yes sir."

"We'll see, on my command, fall out," and disappeared in a pop and a cloud of smoke.

"Alright squad," Naruto stated turning to his squad." Quick bite then Hokage Tower ASAP, let's makes a good impression for or new commanding officer, so at 0 five forty five hours report to the tower."

"Rodger squad leader," Rika chimed before the squad of five dashed off to grab a bite to eat.

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Naruto arrived at his apartment in less than a minute. Unlocking the door in a flurry he grabbed a cup of instant ramen and started boiling water with a quick katon jutsu.

After destroying his meal he grabbed five storage scrolls containing two weeks' worth of MREs (Meals Ready to Eat) and slipped them into a pocket designed to carry scrolls. With that done he grabbed a larger scroll and strapped it under his tanto before donning a black cloak and was out the door.

The blue eyed blond arrived at the tower with five minutes to spare. He stopped outside the entrance snapping to attention and saluting the ANBU with the tiger mask waiting outside.

Returning the salute the ANBU called at ease before telling him to relax.

"Relax, cadet." Seeing Naruto relax he noticed he was already ready to depart for a mission. "Standard equip?" the ANBU asked.

"Negative sir," Naruto replied pulling out the storage scrolls," I brought food enough for my squad to each have two weeks' worth, sir."

"Very good cadet, now let's see if your squad is as prepared."

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Five minutes later the other members arrived dead on time, snapping to attention and saluting which Naruto joined in on as well. Returning the salute he watched the four form up in front of him with Naruto to his left and two steps behind.

"Standard equip?" he asked noticing the four were equipped similar to their squad leader.

"Sir, yes sir."

"Excellent," he replied nodding his head, "Well lets receive our mission details and as you're all already prepared we'll head out after the briefing."

Naruto couldn't help a brief smile under his mask at the small praise before falling into the front of the small formation and marching into the tower behind the ANBU agent.

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The five ninjas to be fell in at attention in front of the Hokage before saluting and muttering a 'Good morning, Hokage-sama.' The Sandaime Hokage was old… nearing some seventy years old which as a ninja was an astounding feat. The gruff elderly man behind the desk had sharp dark brown eyes and a small grey goatee.

The man known as 'the professor' or better known 'the god of shinobi' simply demanded respect.

The only person to ever hold the mantle of Kage twice and knew almost every jutsu the world over.

The Hokage stood from behind his desk and saluted the cadets; he then called at ease and sat back at his desk.

"Squad N," the Hokage mused." The land of Wave as sent a request for aid. Bandits have been encroaching on the small village and economically destroying it. You're mission will be to eliminate all hostiles and any others you see fit taking advantage of the situation. The mission is deemed high C rank due to possibility of ronin presence."

"Do you and your squad accept Uzumaki?"

"Yes, Hokage-sama."

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**AN: Well what did you think? I don't really know how well this will play out but I like it a lot. So give me some feedback and encouragement so I'll be more inclined to write and also let me know if you like the idea.**

**The first part of the story will revolve around Naruto and the remaining year in the ROOT program maybe even diverging a little into his joining ANBU.**

**Every member is at best Chuunin level and will be receiving only C rank missions. Yes he's eight but Kakashi was a Chuunin at eight or nine and Itachi was as well and he made ANBU captain at age thirteen. **

**Also any narratives will be made from Naruto's own knowledge.**

**The dawn really just pertains to it being the beginning of the story, no ominous foreshadowing. **

**The more reviews the better, I'm not a very confident writer and my other stories are pretty much crap and any ideas for FG are pretty much gone since I wrote that before I went to basic training so it's not going anywhere…**

**Hope you enjoyed R&R please!!!**


	2. The Rain

**AN: Here's the next chapter, it should cover the majority if not all of the Wave arc. **

**Oh and wedge formation is simply N**

**I D**

**N R**

**The initials match up to the placement by first name as well.**

**Short and sweet, just the way I like it.**

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**ROOTS OF THE TREE**

Chapter 2

The Rain…

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The five young shinobi to be approached the gate with their supervising ANBU agent.

"Alright," The ANBU spoke getting the squad's attention, "once we leave the gate you'll be on your own. Should the mission call for it, I am an available resource; however, do try to complete the mission without my assistance. Now it's your lead Uzumaki."

"Yes sir. Alright squad I want a standard wedge formation, I'll take point with Yamanaka on my left and Aburame on my right. Hyuuga, take Yamanaka's left and Uchiha take Aburame's right. Now move out."

The four instantly fell in and took off out the gate after their squad leader, the ANBU trailing only slightly behind.

"Neji, Rika," Naruto called over the rushing wind, "If anything seems suspicious activate your doujutsus and alert the rest of the squad."

"Rodger squad leader," the two replied as they leapt through the trees.

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An hour after leaving the gates, rain started crashing down around them. Pulling their cloaks a little tighter to hold off the cold the group increased their pace. Wave was still a day away at this pace.

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Besides the rain, nothing special happened on the way to Wave.

The group arrived at twenty-two hundred hours wet and exhausted from running a whole day in the rain.

Naruto turned to his squad examining their exhausted state. Being a Jinchuriki let alone of the Kyuubi no Kitsune had its benefits almost unlimited chakra and stamina both.

"Uchiha, Yamanaka," he ordered, "go locate an inn for the duration of the mission, 1000 ryu allowance."

Pulling out the mission scroll he called out to Neji and Disasuke, "We will be locating the client a Tazuna-san, and getting any updates on the situation."

The two nodded and walked behind Naruto to where the directions said the house could be found.

As the three walked through the small village they noticed the tell-tale signs of an economic depression. People still had money; still had food, but luxuries were none. People seemed strained and hurried and exhausted.

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The shinobi to be, found the house a few minutes later a little outside of the village. A man with black hair sat on the front steps of the porch a small knife held loosely in his grasp.

The group purposely made noise as they approached to alert the man of their presence.

"Is this the house of Tazuna-san" Naruto asked walking up to the man. The man stood up abruptly and brandished the knife.

"Y-yes, and who are you." He sputtered at the three.

"We are shinobi of Konoha, here in response to Tazuna-san's request for aid."

"Oh," was the intelligent reply as he put his knife away, "well alright come in. My name is Kaiza and I'll bring you to Tazuna."

The man Kaiza brought them into the house and led them into a furnished area where an elderly man sat drinking sake.

"Are you the Shinobi I asked for," he slurred out.

"Yes sir, Tazuna-san." Naruto replied with a nod.

The old man raised a brow at the apparent age but let it slide, who knew with these shinobi these days, kids a little older than your grandson killing for a living.

Naruto then pulled out a map and handed it to Tazuna, "Tazuna-san if you would, please mark the areas the bandits are positioned and my team and I will eliminate them. Also note any other threats and those will be taken care of as well."

Tazuna once again raised a brow at how easy the boy spoke of eliminating but once again didn't say anything. He took out a pen and marked three areas on the map

"These are the camps" he spoke," however the bandits are controlled by a man named Gato. You may know of him as business tycoon, but in reality he makes money embezzling money out of Wave, leaving us poor."

"He also sells our women and uses our boats for shipping drugs. That man is evil; however his death was not in the request. If you can take out the bandits we will be able to take care of him."

"Understood sir," Naruto replied before taking the map and leaving the building.

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"Hyuuga," Naruto turned to Neji as they made their way through the village," locate Yamanaka and Uchiha."

Neji nodded before, with a burst of chakra, activating his byakugan.

"A building only about forty meters ahead of us called 'the waterlog'."

"Weird name," Naruto mumbled to himself to which the other two just shrugged.

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The boys walked into the inn and met the girls near the front desk.

"So this is it," Naruto asked the girls.

"Yes, room 112," Rika confirmed tossing him the keys.

The five left the front steps and went down a hallway on the left reaching room 112.

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"So, what's the plan," Rika muttered after the door was shut.

Naruto turned to his squad and pulled out the map lying it down on the bed, "Tomorrow at 0 five hundred hours, we will begin routing the different camps."

He pointed to the northern most point a little outside the boundaries of the village.

"Uchiha and I will hit point A, the rest of you will hit point C here on the eastern border of the village. At 0 six hundred hours we will regroup and attack point B to the west together."

Naruto then turned to the ANBU hidden in the corner of the room.

"Sir."

"Yes, Uzumaki," the ANBU asked.

"I would like your assistance. While not in the mission perimeters, we were given permission to eliminate any threats." At seeing the ANBU agent nod he continued, "The bandits are controlled by Gato of Gato enterprise, I would like for you to assassinate him tonight before we move out in the morning."

The ANBU shifted his hand to his chin and struck a thinking pose. "Well it is your mission so it's your call, and Hokage-sama gave you leeway. Very well, I should be back around 0 one hundred hours."

He checked his watch before adding, "Right now I have twenty-two-four-five hours. If I'm not back before you move out, investigate the residence but take no action."

"Yes sir, I'll keep watch till 0 one hundred or until you get back." Naruto replied before setting himself up at a desk and memorizing the terrain from the map.

'_Already a good leader_,' the ANBU thought to himself as he jumped out the window to search for Gato's whereabouts.

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A few minutes before one, the ANBU leapt back into the room through same window he used to exit.

When he entered Naruto was still at the desk reading over the map.

The ANBU cleared his throat catching Naruto's attention before speaking.

"I successfully assassinated Gato and eliminated any hostiles in the area. After you clear points A, B, and C we can return to Konoha."

He paused for a second before adding, "The rest will be up to you."

Naruto simply nodded before waking Neji to keep watch, while not really necessary in a non–shinobi village… complacency kills.

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The nest morning Naruto woke up silently and, skipping his rituals, donned his gear. He had only had a three hours of sleep waking up at 0 four hundred hours, but a few can be better than a lot, you're simply more aware.

He left the room no doubt waking the others up to get ready and waited outside in the cool air. The stars where nice here not like in Konoha where the blue glow of lights snuffed out the star shine, Wave was simpler, less electricity and less lights so the stars shone brightly in the sky.

A few minutes later he was joined by the rest of his squad and the ANBU agent.

"Alright," Naruto began," Hyuuga, you're in charge of group two and will attack point C. Uchiha, your with me to point A."

He gave Neji a brief of the terrain near point C and added one last comment before splitting up and heading to their separate points.

"No unnecessary risk, your lives are more important than any mission and never leave a comrade behind."

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Naruto and Rika took off from the others reaching their destination in only a few minutes. They still had some time before the attack was scheduled to happen so they simply observed the enemy.

The camp was… for lack of a better word. Pathetic. There was maybe fifteen bandits and none of them had any idea how to use chakra. Hell only one of them was awake and he didn't seem like he would be for very much longer.

Naruto couldn't help a small smirk as the time shifted to 0 five hundred and he gave the signal to Rika for the attack to begin.

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A man under the employ of Gato sat beside a fire. He was the watchmen and he had been up all night so when the kunai went into the back of his head and he slumped to the ground the thought of being dead didn't even pass his mind.

Naruto and Rika crept through the silently sleeping camp. Neither had killed before but it was expected of them and they had no qualms when it came to duty.

The pair simply held a hand over the victim's mouth as they slit their throats and ended the men's lives.

Ten minutes later they camp was empty of the living besides the two intruders and not one of them had known until they were already dead.

Naruto motioned to Rika and the two took off towards point B to wait for Neji's group.

Neji's group was only twenty minutes Naruto's. It seemed their guard had been more observant and had managed to alert a few others. The battle was over relatively quick still but Disasuke took a graze to the shoulder, nothing more than a shallow cut.

The group waited for the allotted time to begin before attacking. The sun was just starting to rise and with it a few of the bandits. The camp only consisted of thirty or so bandits no more skilled than any of the others and to this squad they would fall like wheat to the scythe.

With the strike started Naruto dashed forward decapitating a man from behind and brining his tanto back around into the kidney of another.

Twelve bandits fell to the preemptive strike, but now they other were awake and ready at the sight of their dead comrades.

Neji, with his byakugan active, danced around the enemies felling them with gentle taps of his fingers. Taps that sent pulses of chakra into the body destroying internal organs.

Naruto not wishing to waste chakra simply stuck to his tanto delivering fatal blow after blow with Ino right after him tanto flashing in the morning rays.

Rika activated her level one sharingun and started sealing, a few seconds later unleashing a grand fireball jutsu and burning the camp down around them.

Disasuke simply stood back and had his kikaichu devour the meager chakra of anyone who managed to escape the onslaught.

Stabbing a man through the heart and kicking him into the burning remains of the camp, Naruto sighed before whipping the blood off his tanto on the clothes of a dead bandit before sheathing it.

He turned to his squad as they cleaned their equipment as well, "Alright squad, form up on me, were heading back to the inn."

Receiving a nod, Naruto dashed off towards the inn with the rest of his squad following.

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**AN: I guess I'll end it there for now. Not too actioney but I'm not too competent at fight scenes and this was more of a slaughter.**

**Just some tidbits but Gato is dead, Kaiza lives, Uchiha massacre doesn't or hasn't happened yet, not sure which. There's simply no need for the coup, and screw Danzo and his crazy sharingun arm. Seriously wtf.**

**I left out the assassination scene simply because Naruto's squad isn't involved and it serves little to no plot development. That and I would probably do a terrible job at it.**

**Anything you're confused on just PM me and I'll be more than happy to fix and or explain. **

**Special thanks to ShadowFang1412, first and only review so far, thanks for the encouragement and hope this chapter didn't disappoint.**

**Read Enjoy and Review please**


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